<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ <!-- J2SE version needed for webstart launch -->
+ <property name="j2sev" value="1.6+"/>
<!-- build directory configuration -->
<property name="libDir" value="lib" />
<property name="resourceDir" value="resources" />
<!-- codebase="http://www.jalview.org/jalview/webstart" -->
<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
+ <jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="logo_big.gif" />
+ <offline_allowed />
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>-->
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="10M" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
<information>
<title>Jalview</title>
<description kind="short">Jalview</description>
<icon href="logo_big.gif" />
<offline_allowed />
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="10M"/>
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+
+ <jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="logo_big.gif" />
+ <offline_allowed />
<!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fa"/>
<association mime-type="application-x/ext-file" extensions="fasta"/>
<association mime-type="application-x/ext-file" extensions="fastq"/>
<association mime-type="application-x/ext-file" extensions="blc"/>
<association mime-type="application-x/ext-file" extensions="aln"/>
<association mime-type="application-x/ext-file" extensions="pir"/>
<association mime-type="application-x/ext-file" extensions="amsa"/>
- -->
+ <association mime-type="application-x/ext-file" extensions="stk"/>-->
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="10M" />
+ <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<all_permissions />
</security>
</jnlp>
- <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
<information>
<title>Jalview</title>
<description kind="short">Jalview</description>
<icon href="logo_big.gif" />
<offline_allowed />
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- -->
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
+ <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<all_permissions />
</security>
</jnlp>
- <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
+ <jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
<information>
<title>Jalview</title>
<vendor>The Barton Group</vendor>
<icon href="logo_big.gif" />
<offline_allowed />
<!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
-->
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
+ <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="logo_big.gif" />
+ <offline_allowed />
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
<TITLE>Applet Parameters</TITLE>
<!-- InstanceEndEditable --> \r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r<style type="text/css">\r<!--\rtd {\r font-family: Geneva, Arial, Helvetica, sans-serif;\r font-size: 12px;\r}\r.plain {\r font-family: Verdana, Arial, Helvetica, sans-serif;\r font-size: 14px;\r text-decoration: none;\r}\r.plain:hover{\r background-color:#000000; color: #F2F2FF;\r}\r \r-->\r</style>\r\r<script language="JavaScript">\rfunction genHref()\r{\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\rfor(i=0; i<8; i++)\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }\rwindow.location=href;\r}\rfunction getEventTarget(e)\r{\rif(!e)\re = window.event;\rif(e.target)\rreturn e.target;\rreturn e.srcElement;\r}\r\r</script>\r</head>\r\r<body alink="#000000" vlink="#000000" link="#000000">\r<script type="text/javascript">\rvar gaJsHost = (("https:" == document.location.protocol) ? \r"https://ssl." : "http://www.");\rdocument.write(unescape("%3Cscript src='" + gaJsHost + \r"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r</script>\r<script type="text/javascript">\rtry{\rvar pageTracker = _gat._getTracker("UA-9060947-1");\rpageTracker._trackPageview();\r} catch(err) {}\r</script>\r<div align="left"> \r <table width="805" height="100" cellpadding="5">\r <tr>\r <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>\r </tr>\r </table>\r <table width="805" border="0" cellpadding="5" cellspacing="5">\r <tr> \r <td width="183" valign="top" bgcolor="#F2F2FF" border="5"> \r \r <div align="center">\r <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">\r <tr> \r <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="applets.html" class="plain">Applet \r Version</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>\r </tr>\r <tr>\r <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release \r history</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source \r Code</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News \r Mailing List</a></td>\r </tr>\r <tr>\r <td align="left" valign="middle"><a\r href="http://www.jalview.org/mailman/listinfo/jalview-discuss"\r class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and\r bug reports to the discussion list.</em></td>\r </tr>\r <tr></tr>\r <tr>\r <!--<td align="left" valign="middle"><br>\r Please send problems<br>and\r bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->\r </tr>\r </table>\r\r </div>\r\r <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>\r <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a> \r </div>\r </td>\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p><strong>Download the applet jar file from <a
- href="jalviewApplet.jar">here</a>. Parameters are described
- <a href="#parameters">below</a>, and the javascript API is described <a href="jalviewLiteJs.html">here</a></strong>.
- </p>
+ <p>\r <strong>Quick Links:<ul><li>Download the applet jar file from <a\r href="jalviewApplet.jar">here</a>\r </li>\r <li>Parameters are described <a href="#parameters">below</a></li>\r <li>The javascript API is described <a\r href="jalviewLiteJs.html">here</a></li>\r </ul></strong>\r </p>\r
<h3 align="left">Useful to know!!</h3>
<ul>
<li>Package all your data files into a single (or multiple) zip / jar
button by setting the embed parameter to true;<br>
<param name="embedded"
value="true"> </li>
- </ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r <ul>\r <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>\r <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>\r </li>\r <li><font size="2">New <a href="jalviewLiteJsApi.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r </font></li></ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r <ul>\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r the jar file in the applet archive argument thus:<br>\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>\r </li>\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have \r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the \r original Jalview structure viewer will still be available. <br>\r </li>\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r the Jmol binary distribution available at the Jmol Sourceforge site, \r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>\r </ul>
+ </ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.7</font></strong></p>\r <ul>\r <li><font size="2">Javascript callbacks capabilities<ul><li>oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.</li>\r <li>To use javascript callbacks, ensure the applet tag includes the '<a href="http://download.oracle.com/javase/6/docs/technotes/guides/plugin/developer_guide/java_js.html">mayscript</a>' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).</li></ul></font>\r </li>\r <li><font size="2">New <a href="jalviewLiteJs.html">jalviewLite java api</a> methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.\r </font></li></ul>\r <p><strong><font size="2">**NEW FEATURES** in Jalview 2.6</font></strong></p>\r <ul>\r <li><font size="2">Jmol compatibility updated to Jmol 12.1.x series - <a href="JmolApplet-12.1.13.jar">download the JmolApplet here</a></font></li>\r<li>To use Jmol as the structure viewer for Jalview, you must include \r the jar file in the applet archive argument thus:<br>\r <pre><font size="2">archive="jalviewApplet.jar,Jmol-12.1.13.jar"</font></pre>\r </li>\r <li>Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have \r Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the \r original Jalview structure viewer will still be available. <br>\r </li>\r <li>Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from \r the Jmol binary distribution available at the Jmol Sourceforge site, \r or <a href="JmolApplet-12.1.13.jar">download the Jmol applet from here</a></li>\r <li><font size="2">Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).</font></li>\r </ul>
<br><strong><font size="2">**NEW FEATURES** in Jalview 2.5</font></strong></p>\r <ul>\r <li><font size="2">New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.</font></li>\r </ul> \r <br><strong><font size="2">**NEW FEATURES** in Jalview 2.4</font></strong></p>
<ul>
<li><font size="2">New applet API methods for feature display control, views, and obtaining current selection via javascript.</font></li>